1 data prep spatial layers

read in some data A and data B. Modify some things, and save as layer 1.

2 data prep other layers

This sources a script that modifies another new layer (tableC) and saves it as table2 and table3, external to the direct Rmd path. It also sources a separate script that reads a previously-saved layer (table 1) and gapfills, saving as table1a.

3 model

sourced script reads in layers 1a, 2, and 3, and does some stuff, and saves the results as layers D and E.

3.0.1 using peek_csv: check to see if tablex.csv shows up in the log?

	loiczid	mean_cat_score	mean_popn_trend_score	n_cat_species	n_trend_species	source
1	49060	0.205263	-0.136364	57	441	aquamaps
2	49061	0.203279	-0.141304	61	46	aquamaps
3	49780	0.171963	-0.153226	107	62	aquamaps
4	49781	0.181818	-0.150000	99	60	aquamaps
5	50494	0.150781	-0.146154	128	65	aquamaps

file_name	file_dir	filetype	uncomm_chgs	commit_hash
tablex.csv	.	input	FALSE	c462f1b

4 The next section (below the divider) is the footer, knitted as a child

The code for the R code chunk header looks like this:

{r child = file.path(dir_git, 'src/templates/ohibc_prov_ftr.Rmd')}

Note that it is executed as if it were just part of this main document; it numbers the section (“Provenance”) as a continuation of the numbering, and the variables are evaluated in the environment of the main document.

5 Provenance

Run ID: 12 (6cb645b); run tag: “standard run”
Run elapsed time: 9.326 seconds; run memory usage: NA MB
System info: System: Darwin, Release: 15.4.0. Machine: x86_64. User: ohara.
Session info
- R version: R version 3.2.2 (2015-08-14), Platform: x86_64-apple-darwin13.4.0, Running under: OS X 10.11.4 (El Capitan).
- Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
- Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3

Provenance summary for run 12 (6cb645b): standard run (Wed May 4 11:20:45 2016)
file_name	file_dir	filetype	uncomm_chgs	commit_hash
table1.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	893b676
table1a.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table2.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
table3.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	a7e123b
tableA.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	8b48c04
tableB.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
tableC.csv	/Users/ohara/github/ohibc/rmd_testing	input	FALSE	00b6e10
table1.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	893b676
table1a.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table2.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
table3.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableD.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
tableE.csv	/Users/ohara/github/ohibc/rmd_testing	output	FALSE	a7e123b
0_sample_script.Rmd	/Users/ohara/github/ohibc/rmd_testing/.	parent_script	TRUE	725220e
1_data_prep_sample.R	.	sourced_script	FALSE	725220e
1a_gapfill.R	.	sourced_script	FALSE	725220e
2_model_sample.R	/Users/ohara/github/ohibc/rmd_testing	sourced_script	FALSE	725220e

R Markdown test rmd